The PhD defence will be partially digital, in Kristen Nygaards sal (5370), Ole Johan Dahls hus, and streamed directly using Zoom. The host of the session will moderate the technicalities while the chair of the defence will moderate the disputation.
Ex auditorio questions: the chair of the defence will invite the attending audience at Kristen Nygaards sal (5370), Ole Johan Dahls hus to ask ex auditorio questions.
Trial lecture
Time and place: May 20, 2026 11:15 AM. Kristen Nygaards sal (5370), Ole-Johan Dahls hus/Zoom.
Main research findings
Gene regulation coordinates cell-type differences through ensuring that the correct genes are expressed at the correct time and in the correct amounts in each cell type. Transcription factors (TF) are proteins that contribute to this process by recognizing and binding DNA to initiate or inhibit gene expression in a highly specific manner. The individual properties, functions, and cooperation of TFs have been studied in various contexts, including human diseases. These studies rely on database and software resources, which need to be functionally correct and well-maintained to ensure reproducibility and reliability of past and future research findings. One such database is the JASPAR database which stores models to predict the DNA-binding preferences of TFs. The research-supporting software resources are varied, encompassing analysis pipelines, machine learning models, simulation tools, and more.
The work behind this thesis aims to support gene regulation studies through modernizing the software infrastructure behind the bi-yearly update of the JASPAR database, the development of robust and easy-to-use data analysis pipelines, and the creation of a novel simulation software to support TF-binding model evaluation. Beyond the actual implementations, the thesis contributes to the discussion on practices and approaches to improve the quality of research software.
Adjudication committee
- Professor Marcel H. Schulz, Goethe University and Uniklinikum Frankfurt, Germany
- Professor Anna-Lena Lamprecht, University of Potsdam, Germany
- Professor Lex Nederbragt, University of Oslo, Norway
Supervisors
Associate Director Anthony Mathelier, Norwegian Centre for Molecular Biosciences and Medicine, University of Oslo
Professor Geir Kjetil Sandve, Department of Informatics, University of Oslo
Chair of defence
- Professor Xing Cai, Department of Informatics, University of Oslo, Norway
Contact information at Department: Pernille Adine Nordby